72709 - Advanced Genomic in Animal Production

Learning outcomes

Student knows high-throughput technologies to identify genes involved in production and reproduction traits in livestock species. Student understands the methodologies for functional and stuctural genomics for improving the efficiencies of breeding schemes. Students knows the most common bioinformatics resources used in animal breeding.

Course contents

The course will be divided into two educational modules of 24 hours each.

In Module 2, the program is structured as follows:

Introduction: Contextualization of production systems aimed at meat and milk production; peculiarities of Italian sectors; production categories. The student will need to learn the correct application of different production systems and recognize the species and breeds raised.

Phenomics: Technologies available for data acquisition in barns; precision livestock farming; sensors; management, processing, and interpretation of big data. The student will be able to describe the technologies currently available for monitoring herds/livestock and the key phenotypes for achieving selection objectives within each sector.

Genome Mapping: DNA and genes; linkage; genetic mapping; physical mapping; markers. The student will be able to calculate the map distance between two loci, distinguish physical maps from genetic maps, and learn which types of markers are useful in modern genetic improvement.

Genome Sequencing: Sanger method; Next Generation Sequencing. The student will know the different techniques currently in use for sequencing portions of DNA or entire genomes and will be able to evaluate their pros and cons.

Practical Activities: Exercise in the computer lab: introduction to bioinformatics for genomic data analysis. The student will learn the basic procedures for inspecting and quality controlling data from genotyping (case study). The student is required to produce a report on the application of genomic data to be presented in class in groups at the end of Module 1 lessons. These activities include a field trip to a human genetics laboratory.

In Module 1, the program is structured as follows:

Trait-Genotype Association: The DNA-chip. Candidate gene approach and genome-wide association studies. The student will learn the DNA-chip technology for genotyping and the different approaches useful for estimating the association of genetic markers with traits of zootechnical interest.

Phenotyping Techniques: Collection of information useful for animal genetic improvement. Large-scale data measurement. The student will learn the methods of collecting important phenotypes within a selection program and will know advanced methods for generating animal information using high-throughput techniques.

Similarity Between Individuals: Genetic and genomic relationship, inbreeding. Relationship matrices important in animal genetic improvement. The student will learn how to estimate the degree of genetic and genomic similarity between individuals in populations subject to breeding programs and the different relationship matrices used to estimate an individual's breeding value.

Animal breeding: Quantitative traits, the animal model and its components. Methods for estimating the breeding value of animals; response to selection and association between traits, genomic selection, and related applications. The student will learn to estimate variance components and how to estimate the breeding value of a breeding candidate; will know how to evaluate a genetic improvement program.

Other Applications of Animal Genomics: Genomics for the study of livestock biodiversity, inbreeding depression, genomic inbreeding, and run of homozygosity. Genomics for the study of traceability of animal products. The student will learn how genomics can be used for managing populations subject to selection programs; will know the different levels of genetic traceability and the various genomic methods useful for ensuring the authenticity of animal products.

Readings/Bibliography

Slides, lectures notes and scientific papers provided during the course.

 

The following books are suggested for more details of lectures topics:

Genetica animale - applicazioni zootecniche e veterinaria. Giulio Pagnacco, casa editrice Ambrosiana.

Genomi 4. T.A. Brown, casa editrice EdiSES.

 

The material presented during the lectures will be available in VITUALE website (https://virtuale.unibo.it/); password for accessing the material is available upon request and at the beginning of the lectures.

Teaching methods

Frontal lectures, seminars and individual/groups practical activities.

Assessment methods

The final exam is written and unique for both modules and is done using EOL platform (https://eol.unibo.it/), with both multiple-choice and open questions. Multiple-choice questions are 10 and each correct answer is evaluated +1 points, 0 for each wrong or missing answer. Open questions are 10 and each correct answer is evaluated +2, 0 for each wrong or missing question. Additionally, up to 4 bonus points can be earned through the presentations of the assignments from Module 2 exercises.

Time given to complete the exam is 90 minutes. During the exam no support, such as textbooks, notes, are allowed.

The maximum evaluation 30/30 cum laude. The exam is passed with a final evaluation of at least 18/30.

Teaching tools

Lectures will be given in the classroom using PowerPoint Presentations, videoprojectors and Microsoft Teams.

Office hours

See the website of Giulio Visentin

See the website of Angela Costa